f12330810d
* fixes to Rmd from Daniela's errata * synced the notebooks * syncing notebooks * all but Chapter10 * chapter 10
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586 lines
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---
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jupyter:
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jupytext:
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cell_metadata_filter: -all
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formats: ipynb,Rmd
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main_language: python
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text_representation:
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extension: .Rmd
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format_name: rmarkdown
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format_version: '1.2'
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jupytext_version: 1.16.7
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---
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# Multiple Testing
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<a target="_blank" href="https://colab.research.google.com/github/intro-stat-learning/ISLP_labs/blob/v2.2/Ch13-multiple-lab.ipynb">
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<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
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</a>
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[](https://mybinder.org/v2/gh/intro-stat-learning/ISLP_labs/v2.2?labpath=Ch13-multiple-lab.ipynb)
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We include our usual imports seen in earlier labs.
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```{python}
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import numpy as np
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import pandas as pd
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import matplotlib.pyplot as plt
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import statsmodels.api as sm
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from ISLP import load_data
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```
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We also collect the new imports
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needed for this lab.
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```{python}
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from scipy.stats import \
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(ttest_1samp,
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ttest_rel,
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ttest_ind,
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t as t_dbn)
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from statsmodels.stats.multicomp import \
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pairwise_tukeyhsd
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from statsmodels.stats.multitest import \
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multipletests as mult_test
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```
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## Review of Hypothesis Tests
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We begin by performing some one-sample $t$-tests.
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First we create 100 variables, each consisting of 10 observations. The
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first 50 variables have mean $0.5$ and variance $1$, while the others
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have mean $0$ and variance $1$.
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```{python}
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rng = np.random.default_rng(12)
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X = rng.standard_normal((10, 100))
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true_mean = np.array([0.5]*50 + [0]*50)
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X += true_mean[None,:]
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```
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To begin, we use `ttest_1samp()` from the
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`scipy.stats` module to test $H_{0}: \mu_1=0$, the null
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hypothesis that the first variable has mean zero.
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```{python}
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result = ttest_1samp(X[:,0], 0)
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result.pvalue
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```
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The $p$-value comes out to 0.931, which is not low enough to
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reject the null hypothesis at level $\alpha=0.05$. In this case,
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$\mu_1=0.5$, so the null hypothesis is false. Therefore, we have made
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a Type II error by failing to reject the null hypothesis when the null
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hypothesis is false.
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We now test $H_{0,j}: \mu_j=0$ for $j=1,\ldots,100$. We compute the
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100 $p$-values, and then construct a vector recording whether the
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$j$th $p$-value is less than or equal to 0.05, in which case we reject
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$H_{0j}$, or greater than 0.05, in which case we do not reject
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$H_{0j}$, for $j=1,\ldots,100$.
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```{python}
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p_values = np.empty(100)
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for i in range(100):
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p_values[i] = ttest_1samp(X[:,i], 0).pvalue
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decision = pd.cut(p_values,
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[0, 0.05, 1],
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labels=['Reject H0',
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'Do not reject H0'])
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truth = pd.Categorical(true_mean == 0,
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categories=[True, False],
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ordered=True)
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```
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Since this is a simulated data set, we can create a $2 \times 2$ table
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similar to Table~\ref{Ch12:tab-hypotheses}.
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```{python}
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pd.crosstab(decision,
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truth,
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rownames=['Decision'],
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colnames=['H0'])
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```
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Therefore, at level $\alpha=0.05$, we reject 15 of the 50 false
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null hypotheses, and we incorrectly reject 5 of the true null
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hypotheses. Using the notation from Section~\ref{sec:fwer}, we have
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$V=5$, $S=15$, $U=45$ and $W=35$.
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We have set $\alpha=0.05$, which means that we expect to reject around
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5% of the true null hypotheses. This is in line with the $2 \times 2$
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table above, which indicates that we rejected $V=5$ of the $50$ true
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null hypotheses.
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In the simulation above, for the false null hypotheses, the ratio of
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the mean to the standard deviation was only $0.5/1 = 0.5$. This
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amounts to quite a weak signal, and it resulted in a high number of
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Type II errors. Let’s instead simulate data with a stronger signal,
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so that the ratio of the mean to the standard deviation for the false
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null hypotheses equals $1$. We make only 10 Type II errors.
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```{python}
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true_mean = np.array([1]*50 + [0]*50)
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X = rng.standard_normal((10, 100))
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X += true_mean[None,:]
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for i in range(100):
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p_values[i] = ttest_1samp(X[:,i], 0).pvalue
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decision = pd.cut(p_values,
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[0, 0.05, 1],
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labels=['Reject H0',
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'Do not reject H0'])
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truth = pd.Categorical(true_mean == 0,
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categories=[True, False],
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ordered=True)
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pd.crosstab(decision,
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truth,
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rownames=['Decision'],
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colnames=['H0'])
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```
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## Family-Wise Error Rate
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Recall from \eqref{eq:FWER.indep} that if the null hypothesis is true
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for each of $m$ independent hypothesis tests, then the FWER is equal
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to $1-(1-\alpha)^m$. We can use this expression to compute the FWER
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for $m=1,\ldots, 500$ and $\alpha=0.05$, $0.01$, and $0.001$.
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We plot the FWER for these values of $\alpha$ in order to
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reproduce Figure~\ref{Ch12:fwer}.
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```{python}
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m = np.linspace(1, 501)
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fig, ax = plt.subplots()
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[ax.plot(m,
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1 - (1 - alpha)**m,
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label=r'$\alpha=%s$' % str(alpha))
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for alpha in [0.05, 0.01, 0.001]]
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ax.set_xscale('log')
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ax.set_xlabel('Number of Hypotheses')
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ax.set_ylabel('Family-Wise Error Rate')
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ax.legend()
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ax.axhline(0.05, c='k', ls='--');
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```
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As discussed previously, even for moderate values of $m$ such as $50$,
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the FWER exceeds $0.05$ unless $\alpha$ is set to a very low value,
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such as $0.001$. Of course, the problem with setting $\alpha$ to such
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a low value is that we are likely to make a number of Type II errors:
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in other words, our power is very low.
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We now conduct a one-sample $t$-test for each of the first five
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managers in the
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`Fund` dataset, in order to test the null
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hypothesis that the $j$th fund manager’s mean return equals zero,
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$H_{0,j}: \mu_j=0$.
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```{python}
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Fund = load_data('Fund')
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fund_mini = Fund.iloc[:,:5]
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fund_mini_pvals = np.empty(5)
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for i in range(5):
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fund_mini_pvals[i] = ttest_1samp(fund_mini.iloc[:,i], 0).pvalue
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fund_mini_pvals
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```
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The $p$-values are low for Managers One and Three, and high for the
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other three managers. However, we cannot simply reject $H_{0,1}$ and
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$H_{0,3}$, since this would fail to account for the multiple testing
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that we have performed. Instead, we will conduct Bonferroni’s method
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and Holm’s method to control the FWER.
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To do this, we use the `multipletests()` function from the
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`statsmodels` module (abbreviated to `mult_test()`). Given the $p$-values,
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for methods like Holm and Bonferroni the function outputs
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adjusted $p$-values, which
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can be thought of as a new set of $p$-values that have been corrected
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for multiple testing. If the adjusted $p$-value for a given hypothesis
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is less than or equal to $\alpha$, then that hypothesis can be
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rejected while maintaining a FWER of no more than $\alpha$. In other
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words, for such methods, the adjusted $p$-values resulting from the `multipletests()`
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function can simply be compared to the desired FWER in order to
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determine whether or not to reject each hypothesis. We will later
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see that we can use the same function to control FDR as well.
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The `mult_test()` function takes $p$-values and a `method` argument, as well as an optional
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`alpha` argument. It returns the decisions (`reject` below)
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as well as the adjusted $p$-values (`bonf`).
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```{python}
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reject, bonf = mult_test(fund_mini_pvals, method = "bonferroni")[:2]
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reject
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```
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The $p$-values `bonf` are simply the `fund_mini_pvalues` multiplied by 5 and truncated to be less than
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or equal to 1.
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```{python}
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bonf, np.minimum(fund_mini_pvals * 5, 1)
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```
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Therefore, using Bonferroni’s method, we are able to reject the null hypothesis only for Manager
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One while controlling FWER at $0.05$.
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By contrast, using Holm’s method, the adjusted $p$-values indicate
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that we can reject the null
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hypotheses for Managers One and Three at a FWER of $0.05$.
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```{python}
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mult_test(fund_mini_pvals, method = "holm", alpha=0.05)[:2]
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```
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As discussed previously, Manager One seems to perform particularly
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well, whereas Manager Two has poor performance.
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```{python}
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fund_mini.mean()
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```
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Is there evidence of a meaningful difference in performance between
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these two managers? We can check this by performing a paired $t$-test using the `ttest_rel()` function
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from `scipy.stats`:
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```{python}
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ttest_rel(fund_mini['Manager1'],
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fund_mini['Manager2']).pvalue
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```
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The test results in a $p$-value of 0.038,
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suggesting a statistically significant difference.
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However, we decided to perform this test only after examining the data
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and noting that Managers One and Two had the highest and lowest mean
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performances. In a sense, this means that we have implicitly
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performed ${5 \choose 2} = 5(5-1)/2=10$ hypothesis tests, rather than
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just one, as discussed in Section~\ref{tukey.sec}. Hence, we use the
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`pairwise_tukeyhsd()` function from
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`statsmodels.stats.multicomp` to apply Tukey’s method
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in order to adjust for multiple testing. This function takes
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as input a fitted *ANOVA* regression model, which is
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essentially just a linear regression in which all of the predictors
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are qualitative. In this case, the response consists of the monthly
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excess returns achieved by each manager, and the predictor indicates
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the manager to which each return corresponds.
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```{python}
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returns = np.hstack([fund_mini.iloc[:,i] for i in range(5)])
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managers = np.hstack([[i+1]*50 for i in range(5)])
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tukey = pairwise_tukeyhsd(returns, managers)
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print(tukey.summary())
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```
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The `pairwise_tukeyhsd()` function provides confidence intervals
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for the difference between each pair of managers (`lower` and
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`upper`), as well as a $p$-value. All of these quantities have
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been adjusted for multiple testing. Notice that the $p$-value for the
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difference between Managers One and Two has increased from $0.038$ to
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$0.186$, so there is no longer clear evidence of a difference between
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the managers’ performances. We can plot the confidence intervals for
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the pairwise comparisons using the `plot_simultaneous()` method
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of `tukey`. Any pair of intervals that don’t overlap indicates a significant difference at the nominal level of 0.05. In this case,
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no differences are considered significant as reported in the table above.
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```{python}
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fig, ax = plt.subplots(figsize=(8,8))
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tukey.plot_simultaneous(ax=ax);
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```
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## False Discovery Rate
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Now we perform hypothesis tests for all 2,000 fund managers in the
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`Fund` dataset. We perform a one-sample $t$-test
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of $H_{0,j}: \mu_j=0$, which states that the
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$j$th fund manager’s mean return is zero.
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```{python}
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fund_pvalues = np.empty(2000)
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for i, manager in enumerate(Fund.columns):
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fund_pvalues[i] = ttest_1samp(Fund[manager], 0).pvalue
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```
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There are far too many managers to consider trying to control the FWER.
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Instead, we focus on controlling the FDR: that is, the expected fraction of rejected null hypotheses that are actually false positives.
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The `multipletests()` function (abbreviated `mult_test()`) can be used to carry out the Benjamini--Hochberg procedure.
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```{python}
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fund_qvalues = mult_test(fund_pvalues, method = "fdr_bh")[1]
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fund_qvalues[:10]
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```
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The *q-values* output by the
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Benjamini--Hochberg procedure can be interpreted as the smallest FDR
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threshold at which we would reject a particular null hypothesis. For
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instance, a $q$-value of $0.1$ indicates that we can reject the
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corresponding null hypothesis at an FDR of 10% or greater, but that
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we cannot reject the null hypothesis at an FDR below 10%.
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If we control the FDR at 10%, then for how many of the fund managers can we reject $H_{0,j}: \mu_j=0$?
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```{python}
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(fund_qvalues <= 0.1).sum()
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```
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We find that 146 of the 2,000 fund managers have a $q$-value below
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0.1; therefore, we are able to conclude that 146 of the fund managers
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beat the market at an FDR of 10%. Only about 15 (10% of 146) of
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these fund managers are likely to be false discoveries.
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By contrast, if we had instead used Bonferroni’s method to control the
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FWER at level $\alpha=0.1$, then we would have failed to reject any
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null hypotheses!
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```{python}
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(fund_pvalues <= 0.1 / 2000).sum()
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```
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Figure~\ref{Ch12:fig:BonferroniBenjamini} displays the ordered
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$p$-values, $p_{(1)} \leq p_{(2)} \leq \cdots \leq p_{(2000)}$, for
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the `Fund` dataset, as well as the threshold for rejection by the
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Benjamini--Hochberg procedure. Recall that the Benjamini--Hochberg
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procedure identifies the largest $p$-value such that $p_{(j)}<qj/m$,
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and rejects all hypotheses for which the $p$-value is less than or
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equal to $p_{(j)}$. In the code below, we implement the
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Benjamini--Hochberg procedure ourselves, in order to illustrate how it
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works. We first order the $p$-values. We then identify all $p$-values
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that satisfy $p_{(j)}<qj/m$ (`sorted_set_`). Finally, `selected_`
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is a boolean array indicating which $p$-values
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are less than or equal to the largest
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$p$-value in `sorted_[sorted_set_]`. Therefore, `selected_` indexes the
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$p$-values rejected by the Benjamini--Hochberg procedure.
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```{python}
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sorted_ = np.sort(fund_pvalues)
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m = fund_pvalues.shape[0]
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q = 0.1
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sorted_set_ = np.where(sorted_ < q * np.linspace(1, m, m) / m)[0]
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if sorted_set_.shape[0] > 0:
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selected_ = fund_pvalues < sorted_[sorted_set_].max()
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sorted_set_ = np.arange(sorted_set_.max())
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else:
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selected_ = []
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sorted_set_ = []
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```
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We now reproduce the middle panel of Figure~\ref{Ch12:fig:BonferroniBenjamini}.
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```{python}
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fig, ax = plt.subplots()
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ax.scatter(np.arange(0, sorted_.shape[0]) + 1,
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sorted_, s=10)
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ax.set_yscale('log')
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ax.set_xscale('log')
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ax.set_ylabel('P-Value')
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ax.set_xlabel('Index')
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ax.scatter(sorted_set_+1, sorted_[sorted_set_], c='r', s=20)
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ax.axline((0, 0), (1,q/m), c='k', ls='--', linewidth=3);
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```
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## A Re-Sampling Approach
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Here, we implement the re-sampling approach to hypothesis testing
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using the `Khan` dataset, which we investigated in
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Section~\ref{sec:permutations}. First, we merge the training and
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testing data, which results in observations on 83 patients for
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2,308 genes.
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```{python}
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Khan = load_data('Khan')
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D = pd.concat([Khan['xtrain'], Khan['xtest']])
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D['Y'] = pd.concat([Khan['ytrain'], Khan['ytest']])
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D['Y'].value_counts()
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```
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There are four classes of cancer. For each gene, we compare the mean
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expression in the second class (rhabdomyosarcoma) to the mean
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expression in the fourth class (Burkitt’s lymphoma). Performing a
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standard two-sample $t$-test
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using `ttest_ind()` from `scipy.stats` on the $11$th
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gene produces a test-statistic of -2.09 and an associated $p$-value
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of 0.0412, suggesting modest evidence of a difference in mean
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expression levels between the two cancer types.
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```{python}
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D2 = D[lambda df:df['Y'] == 2]
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D4 = D[lambda df:df['Y'] == 4]
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gene_11 = 'G0011'
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observedT, pvalue = ttest_ind(D2[gene_11],
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D4[gene_11],
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equal_var=True)
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observedT, pvalue
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```
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However, this $p$-value relies on the assumption that under the null
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hypothesis of no difference between the two groups, the test statistic
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follows a $t$-distribution with $29+25-2=52$ degrees of freedom.
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Instead of using this theoretical null distribution, we can randomly
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split the 54 patients into two groups of 29 and 25, and compute a new
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test statistic. Under the null hypothesis of no difference between
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the groups, this new test statistic should have the same distribution
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as our original one. Repeating this process 10,000 times allows us to
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approximate the null distribution of the test statistic. We compute
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the fraction of the time that our observed test statistic exceeds the
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test statistics obtained via re-sampling.
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```{python}
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B = 10000
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Tnull = np.empty(B)
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D_ = np.hstack([D2[gene_11], D4[gene_11]])
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n_ = D2[gene_11].shape[0]
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D_null = D_.copy()
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for b in range(B):
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rng.shuffle(D_null)
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ttest_ = ttest_ind(D_null[:n_],
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D_null[n_:],
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equal_var=True)
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Tnull[b] = ttest_.statistic
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(np.abs(Tnull) < np.abs(observedT)).mean()
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```
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This fraction, 0.0398,
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is our re-sampling-based $p$-value.
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It is almost identical to the $p$-value of 0.0412 obtained using the theoretical null distribution.
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We can plot a histogram of the re-sampling-based test statistics in order to reproduce Figure~\ref{Ch12:fig-permp-1}.
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||
```{python}
|
||
fig, ax = plt.subplots(figsize=(8,8))
|
||
ax.hist(Tnull,
|
||
bins=100,
|
||
density=True,
|
||
facecolor='y',
|
||
label='Null')
|
||
xval = np.linspace(-4.2, 4.2, 1001)
|
||
ax.plot(xval,
|
||
t_dbn.pdf(xval, D_.shape[0]-2),
|
||
c='r')
|
||
ax.axvline(observedT,
|
||
c='b',
|
||
label='Observed')
|
||
ax.legend()
|
||
ax.set_xlabel("Null Distribution of Test Statistic");
|
||
|
||
```
|
||
The re-sampling-based null distribution is almost identical to the theoretical null distribution, which is displayed in red.
|
||
|
||
Finally, we implement the plug-in re-sampling FDR approach outlined in
|
||
Algorithm~\ref{Ch12:alg-plugin-fdr}. Depending on the speed of your
|
||
computer, calculating the FDR for all 2,308 genes in the `Khan`
|
||
dataset may take a while. Hence, we will illustrate the approach on a
|
||
random subset of 100 genes. For each gene, we first compute the
|
||
observed test statistic, and then produce 10,000 re-sampled test
|
||
statistics. This may take a few minutes to run. If you are in a rush,
|
||
then you could set `B` equal to a smaller value (e.g. `B=500`).
|
||
|
||
```{python}
|
||
m, B = 100, 10000
|
||
idx = rng.choice(Khan['xtest'].columns, m, replace=False)
|
||
T_vals = np.empty(m)
|
||
Tnull_vals = np.empty((m, B))
|
||
|
||
for j in range(m):
|
||
col = idx[j]
|
||
T_vals[j] = ttest_ind(D2[col],
|
||
D4[col],
|
||
equal_var=True).statistic
|
||
D_ = np.hstack([D2[col], D4[col]])
|
||
D_null = D_.copy()
|
||
for b in range(B):
|
||
rng.shuffle(D_null)
|
||
ttest_ = ttest_ind(D_null[:n_],
|
||
D_null[n_:],
|
||
equal_var=True)
|
||
Tnull_vals[j,b] = ttest_.statistic
|
||
|
||
```
|
||
|
||
Next, we compute the number of rejected null hypotheses $R$, the
|
||
estimated number of false positives $\widehat{V}$, and the estimated
|
||
FDR, for a range of threshold values $c$ in
|
||
Algorithm~\ref{Ch12:alg-plugin-fdr}. The threshold values are chosen
|
||
using the absolute values of the test statistics from the 100 genes.
|
||
|
||
```{python}
|
||
cutoffs = np.sort(np.abs(T_vals))
|
||
FDRs, Rs, Vs = np.empty((3, m))
|
||
for j in range(m):
|
||
R = np.sum(np.abs(T_vals) >= cutoffs[j])
|
||
V = np.sum(np.abs(Tnull_vals) >= cutoffs[j]) / B
|
||
Rs[j] = R
|
||
Vs[j] = V
|
||
FDRs[j] = V / R
|
||
|
||
```
|
||
|
||
Now, for any given FDR, we can find the genes that will be
|
||
rejected. For example, with FDR controlled at 0.1, we reject 15 of the
|
||
100 null hypotheses. On average, we would expect about one or two of
|
||
these genes (i.e. 10% of 15) to be false discoveries. At an FDR of
|
||
0.2, we can reject the null hypothesis for 28 genes, of which we
|
||
expect around six to be false discoveries.
|
||
|
||
The variable `idx` stores which
|
||
genes were included in our 100 randomly-selected genes. Let’s look at
|
||
the genes whose estimated FDR is less than 0.1.
|
||
|
||
```{python}
|
||
sorted(idx[np.abs(T_vals) >= cutoffs[FDRs < 0.1].min()])
|
||
|
||
```
|
||
|
||
At an FDR threshold of 0.2, more genes are selected, at the cost of having a higher expected
|
||
proportion of false discoveries.
|
||
|
||
```{python}
|
||
sorted(idx[np.abs(T_vals) >= cutoffs[FDRs < 0.2].min()])
|
||
|
||
```
|
||
|
||
The next line generates Figure~\ref{fig:labfdr}, which is similar
|
||
to Figure~\ref{Ch12:fig-plugin-fdr},
|
||
except that it is based on only a subset of the genes.
|
||
|
||
```{python}
|
||
fig, ax = plt.subplots()
|
||
ax.plot(Rs, FDRs, 'b', linewidth=3)
|
||
ax.set_xlabel("Number of Rejections")
|
||
ax.set_ylabel("False Discovery Rate");
|
||
|
||
```
|
||
|
||
|